[gmx-users] problem in energy minimisation of dna-protein complex

[Justin A. Lemkul]

nitu sharma wrote:
> Dear all
> 
>                 I am doing simulation of dna -protein complex . in this 
> processing I am getting error in energy minimisation step-
> 
> the error comes like this-
> There were 2 inconsistent shifts. Check your topology
> There were 4 inconsistent shifts. Check your topology
> Steepest Descents:
>    Tolerance (Fmax)   =  1.00000e+02
>    Number of steps    =        10000
> There were 6 inconsistent shifts. Check your topology
> Warning: 1-4 interaction between 1 and 6 at distance 7.731 which is 
> larger than the 1-4 table size 2.000 nm
> These are ignored for the rest of the simulation
> This usually means your system is exploding,

Have a look here:

http://oldwiki.gromacs.org/index.php/blowing_up

-Justin

> if not, you should increase table-extension in your mdp file
> or with user tables increase the table size
> There were 6 inconsistent shifts. Check your topology=         inf, 
> atom= 479
> 
> -------------------------------------------------------
> Program mdrun, VERSION 4.0.3
> Source code file: nsgrid.c, line: 357
> 
> Range checking error:
> Explanation: During neighborsearching, we assign each particle to a grid
> based on its coordinates. If your system contains collisions or parameter
> errors that give particles very high velocities you might end up with some
> coordinates being +-Infinity or NaN (not-a-number). Obviously, we cannot
> put these on a grid, so this is usually where we detect those errors.
> Make sure your system is properly energy-minimized and that the potential
> energy seems reasonable before trying again.
> 
> Variable ci has value -2147483648. It should have been within [ 0 .. 10648 ]
> 
> --------------------------------------------------
> 
> My em.mdp file is like this-
> cpp                 =  /usr/bin/cpp
> define              =  -DFLEXIBLE
> constraints         =  none
> integrator          =  steep
> dt                  = 0.001
> nsteps              =  10000
> ;
> ;       Energy minimizing stuff
> ;
> emtol               =  100
> emstep              =  0.01
> 
> nstcomm             =  1
> nstlist             =  10
> ns_type             =  grid
> rlist               =  1.0
> rcoulomb            =  1.0
> vdw-type            = cut-off
> rvdw                =  1.0
> coulombtype         =  PME
> Tcoupl              =  no
> Pcoupl              =  no
> 
> gen_vel             =  no
> comm-mode           = Linear
> pbc                 = XYZ
>                            
> 
> can anyone suggest how can i get rid from this problem.
> Thanks a lot in advance.
> Nitu sharma
> 
> 
> 
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> 
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-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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